RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4877
(120 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 62.1 bits (152), Expect = 2e-14
Identities = 21/36 (58%), Positives = 27/36 (75%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++Y S +R EL+K L LTE Q+K WFQNRR KWK+
Sbjct: 22 NRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
Score = 50.2 bits (121), Expect = 9e-10
Identities = 18/25 (72%), Positives = 20/25 (80%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+K L LTE Q+K WFQNRR KWK
Sbjct: 32 ELAKKLGLTERQVKVWFQNRRAKWK 56
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 57.6 bits (140), Expect = 1e-12
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 11/61 (18%)
Query: 8 NLTEVQIKT---WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
T Q++ F+ + Y S +R EL+K L LTE Q+K WFQNRR K K+
Sbjct: 6 RFTPEQLEELEKEFEK--------NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57
Query: 65 Q 65
Sbjct: 58 S 58
Score = 46.5 bits (111), Expect = 3e-08
Identities = 17/25 (68%), Positives = 19/25 (76%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+K L LTE Q+K WFQNRR K K
Sbjct: 32 ELAKELGLTERQVKIWFQNRRAKLK 56
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 56.1 bits (136), Expect = 6e-12
Identities = 21/40 (52%), Positives = 26/40 (65%)
Query: 24 KWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
K + Y S +R EL+K L L+E Q+K WFQNRR KWK
Sbjct: 18 KEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
Score = 47.6 bits (114), Expect = 1e-08
Identities = 17/25 (68%), Positives = 20/25 (80%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+K L L+E Q+K WFQNRR KWK
Sbjct: 33 ELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 38.2 bits (89), Expect = 2e-04
Identities = 16/38 (42%), Positives = 25/38 (65%)
Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
++ Y S R++LS LLN+ ++ WFQN+R K KK+
Sbjct: 72 INPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109
Score = 36.6 bits (85), Expect = 7e-04
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK-----YVDKYLSVSKRMELSKLLNLTEVQIKTWFQ 56
+LS LLN+ ++ WFQN+R K K V++ + +L+K+ +L+ QI
Sbjct: 83 KLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPGEEEA-DLAKIGSLSTGQISIIET 141
Query: 57 NRRTK 61
++
Sbjct: 142 LEFSR 146
>gnl|CDD|182099 PRK09831, PRK09831, putative acyltransferase; Provisional.
Length = 147
Score = 29.5 bits (66), Expect = 0.23
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 50 QIKTWFQNRRTKWKKQLASKLKMVA--HNRPTGF 81
QI W Q ++WK++LA VA + +P GF
Sbjct: 34 QIAAWAQIDESRWKEKLAKSQVRVAVINAQPVGF 67
>gnl|CDD|218628 pfam05541, Spheroidin, Entomopoxvirus spheroidin protein.
Entomopoxviruses (EPVs) are large (300-400 nm)
oval-shaped viruses replicating in the cytoplasm of
their insect host cells. At the end of their replicative
cycle EPVs virions are occluded in a highly expressed
protein called spheroidin. This protein forms large
(5-20 mm long) oval-shaped occlusion bodies (OBs) called
spherules. The infectious cycle of EPVs begins with the
ingestion by the insect host of the spherules, their
dissolution by the alkaline reducing conditions of the
midgut fluid and the release of virions in the midgut
lumen. The infective particles first replicate in midgut
epithelial cells, then pass the gut barrier to colonise
the internal tissues, mainly the fat body cells. Whilst
spheroidin has been demonstrated to be non-essential for
viral replication, it plays an essential role in the
natural biological cycle of the virus in protecting
virions from adverse environmental conditions (e.g. UV
degradation) and thus improving transmission efficacy.
In this respect, spheroidins are functionally similar to
polyhedrins of baculoviruses or cypoviruses.
Length = 943
Score = 28.7 bits (64), Expect = 0.74
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 61 KWKKQLASKLKMVAHNRPTGFYFPGG 86
K+ ++ S LK+V H+R TG FPG
Sbjct: 323 KFDSKIKSLLKIVMHDRGTGNVFPGR 348
>gnl|CDD|132368 TIGR03325, BphB_TodD, cis-2,3-dihydrobiphenyl-2,3-diol
dehydrogenase. Members of this family occur as the BphD
protein of biphenyl catabolism and as the TodD protein
of toluene catabolism. Members catalyze the second step
in each pathway and proved interchangeable when tested;
the first and fourth enzymes in each pathway confer
metabolic specificity. In the context of biphenyl
degradation, the enzyme acts as
cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC
1.3.1.56), while in toluene degradation it acts as
cis-toluene dihydrodiol dehydrogenase.
Length = 262
Score = 28.2 bits (63), Expect = 1.1
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 80 GFYFPGGGPLIFGAQH 95
GFY GGGPL A+H
Sbjct: 145 GFYPNGGGPLYTAAKH 160
>gnl|CDD|221375 pfam12008, EcoR124_C, Type I restriction and modification enzyme -
subunit R C terminal. This enzyme has been
characterized and shown to belong to a new family of the
type I class of restriction and modification enzymes.
This family is involved in bacterial defence by making
double strand breaks in specific double stranded DNA
sequences, e.g. that of invading bacteriophages. EcoR124
is made up of three subunits, HsdR, HsdS and HsdM. The R
subunit has ATPase and restriction endonuclease
activity. This domain is the C terminal of the R
subunit.
Length = 269
Score = 28.0 bits (63), Expect = 1.2
Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 8/70 (11%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61
EL++ L E +K + T +L LL + ++ K
Sbjct: 202 ELAEEEGLDEEALKEFIDEYLTGDLNEIPRGD-----DLKDLLPPEK---LKAKFRKKEK 253
Query: 62 WKKQLASKLK 71
KK+L KL
Sbjct: 254 KKKRLNEKLA 263
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 25.9 bits (58), Expect = 1.3
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRR 59
Y S ++ EL++ L+ QI WF N R
Sbjct: 10 YPSEEEKSELARQTGLSRKQIDNWFINAR 38
Score = 24.0 bits (53), Expect = 6.9
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 2 ELSKLLNLTEVQIKTWFQNRR 22
EL++ L+ QI WF N R
Sbjct: 18 ELARQTGLSRKQIDNWFINAR 38
>gnl|CDD|239275 cd02977, ArsC_family, Arsenate Reductase (ArsC) family; composed
of TRX-fold arsenic reductases and similar proteins
including the transcriptional regulator, Spx. ArsC
catalyzes the reduction of arsenate [As(V)] to arsenite
[As(III)], using reducing equivalents derived from
glutathione (GSH) via glutaredoxin (GRX), through a
single catalytic cysteine. This family of predominantly
bacterial enzymes is unrelated to two other families of
arsenate reductases which show similarity to
low-molecular-weight acid phosphatases and
phosphotyrosyl phosphatases. Spx is a general regulator
that exerts negative and positive control over
transcription initiation by binding to the C-terminal
domain of the alpha subunit of RNA polymerase.
Length = 105
Score = 25.9 bits (58), Expect = 3.0
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 15 KTWFQNRRTKWKYVDKYLSVS-KRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
W + +++++D YL + EL +LL + ++ F R T ++K
Sbjct: 16 LAWLEEHGIEYEFID-YLKEPPTKEELKELLAKLGLGVEDLFNTRGTPYRK 65
Score = 24.8 bits (55), Expect = 8.2
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNL 46
EL +LL + ++ F N R Y L+ + + L L
Sbjct: 40 ELKELLAKLGLGVEDLF-NTRGT-PYRKLGLADKDELSDEEALEL 82
>gnl|CDD|152754 pfam12319, TryThrA_C, Tryptophan-Threonine-rich plasmodium antigen
C terminal. This protein is found in eukaryotes.
Proteins in this family are typically between 254 to 536
amino acids in length. This family is the C terminal of
a surface antigen of malarial Plasmodium species. It is
currently being targeted for use as part of a subunit
vaccine against Plasmodium falciparum, the main species
involved in causing human malaria.
Length = 217
Score = 26.1 bits (58), Expect = 4.6
Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 10/63 (15%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62
L K L E Q + W +T+ K K++ + K ++ E + W +W
Sbjct: 62 LKKSLTWDESQWEEWI---KTEGK---KFM----EKDWKKWIDENESNLNKWIVKEWNQW 111
Query: 63 KKQ 65
K +
Sbjct: 112 KNK 114
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 26.4 bits (59), Expect = 4.9
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 8/42 (19%)
Query: 28 VDKYLSVSKRME--------LSKLLNLTEVQIKTWFQNRRTK 61
V+KYL VSK++ + L L E IK+ F+N ++K
Sbjct: 1072 VEKYLEVSKKLAEEYGVSDYTKQRLELLERGIKSLFENDKSK 1113
>gnl|CDD|217869 pfam04065, Not3, Not1 N-terminal domain, CCR4-Not complex
component.
Length = 233
Score = 25.7 bits (57), Expect = 5.7
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAH 75
+K S KR E+ KL L + QIKTW + K K L K++
Sbjct: 41 EKLESDLKR-EIKKLQRLRD-QIKTWLSSSDIKDKDSLLENRKLIET 85
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 26.0 bits (57), Expect = 6.1
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 55 FQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGGPL 89
+++R +WKK+ KL++V H G L
Sbjct: 224 WKDRMEEWKKKQNEKLQVVKHEGGNDGGNNDGDEL 258
>gnl|CDD|187606 cd05348, BphB-like_SDR_c,
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
(BphB)-like, classical (c) SDRs.
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is
a classical SDR, it is of particular importance for its
role in the degradation of biphenyl/polychlorinated
biphenyls(PCBs); PCBs are a significant source of
environmental contamination. This subgroup also includes
Pseudomonas putida F1
cis-biphenyl-1,2-dihydrodiol-1,2-dehydrogenase (aka
cis-benzene glycol dehydrogenase, encoded by the bnzE
gene), which participates in benzene metabolism. In
addition it includes Pseudomonas sp. C18 putative
1,2-dihydroxy-1,2-dihydronaphthalene dehydrogenase (aka
dibenzothiophene dihydrodiol dehydrogenase, encoded by
the doxE gene) which participates in an upper
naphthalene catabolic pathway. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 257
Score = 25.8 bits (57), Expect = 7.1
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 80 GFYFPGGGPLIFGAQHG 96
GFY GGGPL ++H
Sbjct: 144 GFYPGGGGPLYTASKHA 160
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.133 0.410
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,866,989
Number of extensions: 478221
Number of successful extensions: 447
Number of sequences better than 10.0: 1
Number of HSP's gapped: 447
Number of HSP's successfully gapped: 32
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)